Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5') adenosine

Journal of Biomolecular Structure & Dynamics
S C Jain, H M Sobell

Abstract

Ethidium forms a crystalline complex with the dinucleoside monophosphate, uridylyl (3'-5') adenosine (UpA). The complex crystallizes in the monoclinic space group P2l with unit cell dimensions, a = 13.704 A, b = 31.674 A, c = 15.131 A, beta = 113.9 degrees. This light atom structure has been solved to atomic resolution and refined by full matrix least squares to a residual of 0.12, using 3,034 observed reflections. The asymmetric unit consists of two ethidium molecules, two UpA molecules and 19 solvent molecules, a total of 145 non-hydrogen atoms. The two UpA molecules are hydrogen-bonded together by Watson-Crick type base pairing. Base-pairs in this duplex are separated by 6.7 A; this reflects intercalative binding by one of the ethidium molecules. The other ethidium molecule stacks on either side of the intercalated base-paired dinucleoside monophosphate, being related by a unit cell translation along the a axis. The conformation of the sugar-phosphate backbone accompanying intercalation has been accurately determined in this analysis, and contains the mixed sugar-puckering pattern: C3' endo (3'-5') C2' endo. This same structural feature has been observed in the ethidium-iodoUpA and ethidium-iodoCpG complexes, and exists in t...Continue Reading

References

Dec 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·P J BondS J Lippard
Sep 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·H M SobellT D Sakore
Apr 1, 1968·Biopolymers·Donald M Crothers

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Citations

Dec 5, 2015·Biochemistry·Kevin Ka Ki Leung, Brian Herbert Shilton
Mar 18, 2016·Journal of Structural and Functional Genomics·Henry M Sobell
Nov 3, 2006·Biopolymers·Micah J McCauley, Mark C Williams
May 1, 2007·Nature Methods·Ioana D VladescuMark C Williams
Oct 26, 2005·Physical Review Letters·Ioana D VladescuMark C Williams
Dec 14, 2004·Journal of Biomolecular Structure & Dynamics·Poghos O VardevanyanArmen T Karapetian
Oct 5, 1986·Journal of Molecular Biology·T P LybrandP A Kollman
Aug 9, 2011·Journal of Chemical Theory and Computation·Karol M LangnerPeter Pulay
Jul 3, 2018·ACS Combinatorial Science·Hafeez S HaniffMatthew D Disney
Sep 18, 2020·The Journal of Physical Chemistry. B·Joseph TibbsJustin P Peters

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